Run Browser : Browse : Sequence Read Archive : NCBI/NLM/NIH

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR7652956	22.3M	1.1Gbp	413.3M	50.8%	2018-08-18	public

Quality graph (bigger)(smaller)

241

Phred quality score

This run has 2 reads per spot:

L=51, 100%

L=0

Legend

		Technical read
		Application Read
L=4, 100%		Length is 4, 100% spots contain this read
̅L=165, σ=92.8, 66%		Average length is 165, standard deviation is 92.8, 66% spots contain this read

Experiment	Library Name	Platform	Strategy	Source	Selection	Layout	Action
SRX4515365	H_48h_MG_7_rep2	Illumina	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE

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Total RNA was extracted from 5th instar larvae midguts that were dissected at 48 h post mock-inoculation (oral) with 5ul of a 10% sucrose solution containing no virus. Following total RNA extraction using TRIzol reagent (Ambion), strand-specific RNA-Seq libraries were constructed. Briefly, poly(A) mRNA isolated from 3 g of total RNA using oligo(dT)25 Dynabeads (Invitrogen) were fragmented at 94C for 5 min in buffer containing ProtoScript II reaction buffer (NEB), hexamer (Qiagen), and oligo (dT)23 VN (NEB). Subsequently, first-strand cDNA was synthesized using ProtoScript II and second strand synthesis was carried out with a reaction mix consisting of RNase H (NEB), the Klenow fragment of DNA polymerase I (NEB), and dNTP mix with dUTP (dATP, dCTP, dGTP, and dUTP) (Promega Corporation). Further, TruSeq universal adapters were ligated to end-repaired and dA-tailed cDNA fragments. Subsequently, dUTP containing strands were removed and PCR amplification was performed with library-specific TruSeq PCR primers. Following purification and quantification of the libraries, libraries were sequenced on the Illumina HiSeq4000 platform at the CLC Genomics and Epigenomics Core Facility at the Weill Cornell Medical College.

Biosample	Sample Description	Organism	Links
SAMN09769649 (SRS3633928)		Trichoplusia ni	PRJNA484772

Bioproject	SRA Study	Title
PRJNA484772	SRP156551	Global analysis of baculovirus Autographa californica Multiple Nucleopolyhedrovirus (AcMNPV) gene expression in the midgut of the Trichoplusia ni larvae

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The baculovirus AcMNPV is a large dsDNA virus that encodes approximately 156 genes and is highly pathogenic to a variety of larval lepidopteran insects in nature. Oral infection of larval midgut cells is initiated by the occlusion derived virus (ODV), while secondary infection of other tissues is mediated by the budded virus (BV). Global viral gene expression has been studied in detail in BV-infected cell cultures, but studies of ODV-infection in the larval midgut are limited. In this study, we examined expression of the ~156 AcMNPV genes in Trichoplusia ni midgut tissue using a transcriptomic approach. We analyzed expression profiles of viral genes in the midgut, and compared them with profiles from a T. ni cell line (Tnms42). Several viral genes (p6.9, orf76, orf75, pp31, Ac-bro, odv-e25, and odv-ec27) had high expression levels in the midgut throughout the infection. Also, the expression of genes associated with occlusion bodies (polh and p10) appeared to be delayed in the midgut in comparison with the cell line. Comparisons of overall viral gene expression profiles revealed remarkable similarities between the midgut and cell line for most genes, although substantial differences were also observed for some viral genes. These included genes associated with high level BV production (fp-25k), acceleration of systemic infection (v-fgf), and enhancement of viral movement (arif-1/orf20). These differential expression patterns appear to represent specific adaptations for virus infection and movement through the polarized cells of the lepidopteran midgut.

SRA archive data

SRA archive data is normalized by the SRA load process and used by the SRA Toolkit to read and produce formats like FASTQ, SAM, etc. The default toolkit configuration enables it to find and retrieve SRA runs by accession.

Public SRA files are now available from GCP and AWS cloud platforms as well as from NCBI. Access to most data in the cloud requires a user account with the cloud service provider. The user’s account will incur costs for cloud compute or to copy data outside of the specified cloud service region.

Type	Size	Location	Name	Free Egress	Access Type
SRA Normalized	403,637 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7652956/SRR7652956	worldwide	anonymous
SRA Lite	280,711 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/652/SRR7652956.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-1/SRR7652956/SRR7652956.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-102/SRR7652956/SRR7652956.zq.1	gs.us-east1	gcp identity

Original format

The original files submitted to SRA. These files may require specific software to open, read and interpret data.

Type	Size	Location	Name	Free Egress	Access Type
fastq	725,013 Kb	AWS	s3://sra-pub-src-3/SRR7652956/H_48h_R2_S17_L005_R1_001.fastq.gz	-	Use Cloud Data Delivery

Egress and Access: what does it mean?

Egressterm used by cloud providers to describe cost (charged to the user) of moving data outside of the storage region

Free Egress column indicates where the data can be accessed without an egress charge:

worldwide can be downloaded from anywhere for free
s3.us-east-1 is free to access from machines running in Amazon's us-east-1 region, access from other regions or transport outside of AWS will require paying egress charges
gs.US is free to access from machines running in Google’s gs.US region, access from other regions or transport outside of GCP will require paying egress charges

Access Typedescribes whether a cloud service user account is necessary for data access. "anonymous" access means general public access

Namecolumn provides either a link to free download location at NCBI or a URL for the cloud provider storage location. Either s3:// for Amazon or gs:// for Google storage

Why is SRA data in the cloud?

In order to support large scale (hyper parallel) data analyses SRA data is now available at GCP and AWS with few caveats:

SRA data is copied to the cloud from NCBI. There may be a lag between availability from NCBI and from CSP (cloud service providers)
To access public data user account with the cloud service provider is required. Your account will incur costs for cloud compute and/or to copy data (either archival or results of your comute) outside of the specified cloud service region
Distribution of protected data is signed by NIH account and requires user to operate in the same region as the data

SRA has also begun to provide access to originally submitted source files:

not all files have been validated by SRA
not all files have been copied to cloud locations (recovering it from NCBI tape system takes time ).
the volume of this type of data a much larger and it is not used as often so we will keep most of it on tape or "cold" storage in cloud. As a result the data may not be available instantly and restore requests will be served on first-come first-served basis and cost of resore may be charged to your user account.

What is "Cloud Data Delivery"?: Please visit SRA Data Delivery service to request Sequence Read Archive (SRA) data to be delivered to an Amazon Web Services (AWS) or Google Cloud Platform (GCP) bucket of your choice.

Taxonomy Analysis

Unidentified reads: 98.32%
Identified reads: 1.68%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Helicoverpa armigera	species	0.8	9,040
Eukaryota	Spodoptera litura	species	0.5	5,898
Bacteria	Terrabacteria group		0.2	2,752

How to read results?: Results show distribution of reads mapping to specific taxonomy nodes as a percentage of total reads within the analyzed run. In cases where a read maps to more than one related taxonomy node, the read is reported as originating from the lowest shared taxonomic node. So when a read maps to two species belonging to the same genus, it is assigned at the genus level. Sequence reads from a single organism will map to several taxonomy nodes spanning the organism’s lineage. The number of reads mapping to higher level nodes will typically be greater than those that map to terminal nodes.

STAT results are proportional to the size of sequenced genomes. Given a mixed sample containing several organisms at equal copy number, proportionally more reads originate from the larger genomes. This means that the percentages reported by STAT will reflect genome size and must be considered against the genomic complexity of the sequenced sample.

How can I query this analysis data?: Please take a look at NCBI SRA Cloud-based Taxonomy Analysis Table

How taxonomy analysis is done?: A fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next generation sequence submissions

Uninfected Trichoplusia ni midgut at 48 hour post mock-inoculation, replicate 2(SRR7652956)

SRA archive data

Original format

Taxonomy Analysis

Strong signals

Intensity graph

	View: biological readstechnical readsquality scoresadvanced options Hide Read base space color space show separated reads quality score with bases show clipped show 4 channel quality scorewith bases Intensity graph Signals table
	Intensity graph